Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Coarse-Grained Modeling of Electrostatic Interactions in Chromatin
Stockholm University, Faculty of Science, Department of Chemistry.ORCID iD: 0000-0002-9390-5719
Number of Authors: 42025 (English)In: Wiley Interdisciplinary Reviews: Computational Molecular Science, E-ISSN 1759-0884, Vol. 15, no 6, article id e70059Article, review/survey (Refereed) Published
Abstract [en]

The double-helical DNA of large eukaryotic genomes is tightly compacted within the tiny cell nucleus as a DNA–protein complex, chromatin. The universal elements of chromatin, nucleosome core particles (NCPs, 147 base pairs of DNA wrapped around an octamer of histone proteins), are connected by linker DNA of variable lengths into nucleosome arrays, which fold into various and dynamic higher-order structures. Since DNA is a highly negatively charged polyelectrolyte, electrostatic interactions of DNA with positively charged histones, other charged nuclear proteins, as well as with monovalent and multivalent cations, contributes decisively to the formation and folding of nucleosome arrays. The dimensions and timescales of cellular chromatin states and transformations necessitate a multiscale coarse-graining (CG) approach to understand their properties through computational modeling. In this review, we highlight the importance of electrostatics for NCP interactions and nucleosome fiber folding in vitro and in vivo, and argue that the inclusion of explicit ions is indispensable for accurate CG modeling of chromatin structure and dynamics. A summary of the existing CG mapping and force field setups is provided. A brief account of CG modeling studies in which salt dependency is approximated by the Debye–Hückel treatment is given. The primary focus is on the presentation of results from papers that include explicit monovalent and multivalent ionic species in CG simulations of nucleosomes and nucleosome arrays. Finally, we underline perspectives and challenges for future multiscale computational modeling of chromatin.

Place, publisher, year, edition, pages
2025. Vol. 15, no 6, article id e70059
Keywords [en]
chromatin phase separation, chromatin structure, explicit ions, molecular dynamics, nucleosome arrays
National Category
Biochemistry Biophysics
Identifiers
URN: urn:nbn:se:su:diva-250330DOI: 10.1002/wcms.70059ISI: 001625834100001Scopus ID: 2-s2.0-105022810439OAI: oai:DiVA.org:su-250330DiVA, id: diva2:2021486
Available from: 2025-12-15 Created: 2025-12-15 Last updated: 2025-12-15Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textScopus

Authority records

Lyubartsev, Alexander P.

Search in DiVA

By author/editor
Lyubartsev, Alexander P.
By organisation
Department of Chemistry
BiochemistryBiophysics

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 35 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf